Recommendation: Copy the VPS (it is fairly simple) and try N times until your -u all pass clean and PLEASE version first the folders in order to make a proper diff, we expend something like 10 to 40 hours to make clean such job, if no direct modification it is fairly easy.

For future: do not use .deb into production people make huge mistakes patching directly the code and then forget the work done so it sets a dangerous environment.

Note: If you work securely no there are any job you can not go back then.

Final recommendation: If it is your first time doing that I strongly recommend contact somebody with more experience.